Shortly after the creation of the Confederacy, President Jefferson Davis recommended Elmore as its first treasurer, a decision endorsed by the Secretary of the TreasuryChristopher Memminger and ratified by the Provisional Confederate Congress. He took office on March 6, 1861. In his official capacity, Elmore had to receive, count, keep, and disburse government funds in cooperation with the Congress and other agencies. All requisitions drawn upon the national treasury had first to pass Elmore's inspection before they could assume the form of executive warrants. Even a warrant approved by the Comptroller and sanctioned by the Memminger was subject to Elmore's review before being paid.[2]

Memminger resigned his post as Secretary of the Treasury on July 18, 1864, and was replaced by fellow South Carolinian George Trenholm. However, Elmore initially stayed on as Treasurer under Trenholm.

In August 1864, Elmore accused John M. Daniels, the controversial editor of the Richmond Examiner, of slandering him by accusing Elmore and Secretary of StateJudah P. Benjamin of gambling away government funds at a private club. When no retraction was forthcoming from the newspaperman, Elmore demanded a duel. The two opponents met on Belle Isle, and Elmore wounded Daniels with his first shot.[3] One sympathetic former soldier later wrote, "The result of this duel occasioned as many hearty congratulations among the true Confederates in Richmond as if it had been the announcement of a victory by General Lee over the Federal army."[2][4]

Shortly afterward, Elmore resigned his position as Treasurer and was replaced by John N. Hendren on October 10, 1864.

^National Tribune, December 29, 1891. Retrieved 2008-10-07. Daniels was as much depised by the Union prisoners of war held in Richmond as he was by the Confederate soldiers and government officials. One Yankee deemed him "this beast of an editor." The much depised Daniels survived his duel with Elmore, as well as those with nine other men, only to die of natural causes in late March 1865 just before Richmond fell to the Union army.